The present invention relates to the field of imaging. In particular, the present invention provides methods and apparatus for detecting pixel stutter and for improving scanner hardware and software design and scanner manufacturing quality control.
U.S. Pat. No. 5,424,186 describes a pioneering technique for, among other things, forming and using high density arrays of molecules such as oligonucleotide, RNA, peptides, polysaccharides, and other materials. This patent is hereby incorporated by reference for all purposes. In this preferred technique, arrays of oligonucleotides or peptides, for example, are formed on the surface by sequentially removing a photoremovable group from a surface, coupling a monomer to the exposed region of the surface, and repeating the process. These techniques have been used to form extremely dense arrays of oligonucleotides, peptides, and other materials. Such arrays are useful in, for example, drug development, gene expression monitoring, genotyping, and a variety of other applications.
Genetic mutations or gene expression may be detected by specific nucleic acid hybridization. A solution containing one or more targets to be analyzed (i.e., samples from patients) contacts the probe array. The targets will bind or hybridize with complementary probe sequences. Generally, the targets are labeled with a fluorescent marker, radioactive isotopes, enzymes, or other types of markers. Accordingly, locations at which targets hybridize with complimentary probes can be identified by locating the markers. Based on the locations where hybridization occur, information regarding the target sequences can be extracted. The existence of a mutation may be determined by comparing the target sequence with the wild type.
A number of scanning systems, such as the GeneArray® scanner (Affymetrix and Agilent, Calif.) and 428™ scanners (Affymetrix, Calif.), are available for obtaining hybridization images. However, there is still need in the art for methods, software and systems that evaluate the performance of scanning systems.